Cooling in the spent fuel pools was down for a few hours to allow for removal of the rodent carcasses and the installation of a net to prevent future infiltrations.
The event marks the third time in five weeks that spent fuel cooling systems have been shut down due to rodents and comes on top of the discovery of substantial leakage from contaminated water tanks at the facility.
Other recent problems at Fukushima include the 120 tons of contaminated water that are believed to have leaked out of temporary storage tanks.
Fish caught near the plant have had high levels of radiation since the meltdown, during which contaminated water from the facility spilled in to the sea several times, according to reports.
Plant operators have been working to contain damaged to Fukushima plant since the March 11, 2011 earthquake and tsunami caused a trio of meltdowns at the plant.